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Tracking Two Subjects' Microbiomes for a Year, Researchers See Stability, Changes with Diet

NEW YORK (GenomeWeb) – Gut microbial communities are largely stable over time, though they can be shaped by host behaviors such as diet, according to a new sequencing-based analysis appearing in Genome Biology.

Researchers from the Massachusetts Institute of Technology and elsewhere tracked the gut microbiomes of two individuals for nearly a year while also collecting a host of behavioral data.

"On any given day, the amount of one species could change many fold, but after a year, that species would still be at the same median level," Eric Alm, an associate professor of biological and environmental engineering at MIT, said in a statement. "To a large extent, the main factor we found that explained a lot of that variance was the diet."

Alm and his colleagues followed two unrelated male research participants and their microbiomes for nearly a year. Each day, the participants collected stool and saliva samples for analysis. The researchers also provided the participants with an iPhone app to enable them to more easily report health and lifestyle variables such as diet, exercise, illness, mood, and more.

The researchers characterized the participants' samples after quality control checks though high-throughput sequencing of amplified 16S ribosomal RNA, and they grouped the resulting reads into operational taxonomic units based on sequence similarity.

Overall, the researchers found that the gut and saliva microbiome were rather stable. For instance, they noted that between 75 percent and 88 percent of bacteria exhibited stationary dynamics for the timespan they evaluated and that both high- and low-abundance taxa were just as likely to be stationary.

Despite this high-level OTU stability, the researchers noted that the remaining percentage of bacteria that were not stationary appeared to be competing for resources.

But certain events can disturb the stability of the microbiome, Alm and his colleagues noted.

During the course of the study, Subject A moved from a major US city to the capital of a developing nation in Southeast Asia, before returning some 50 days later.

While in Southeast Asia, the researchers noted a number of changes to Subject A's gut microbiome. For instance, they observed an increase in Bacteroidetes clusters and a decrease in Firmucutes clusters while he was abroad. Personal data collected from the participant indicated that his diet changed to match local cuisine while he was there. His gut microbiome returned to its pre-travel state shortly upon his return to the States and prior eating habits.

He also experienced a bout of diarrhea while abroad, and that episode was reflected in his microbiome by an increase in a Proteobacteria-rich cluster.

Subject B, too, had an experience that changed his gut microbiome. Some 150 days into the study, he came down with food poisoning, which was reflected by a spike in Salmonella OTU reads.

After his infection, though, Subject B's microbiome remained changed, the researchers reported, even though he kept similar eating habits as before his infection.

Some OTUs that accounted for only 15 percent of his pre-infection reads increased to be 65 percent of his post-infection reads. Similarly, some OTUs that previously made up 44 percent of pre-infection reads plummeted to less than 1 percent after his infection.

Unlike Subject A, though, Subject B's microbiome never quite returned to its pre-event state. The researchers speculated that different bacteria with similar functions took over the roles of the taxa that were lost during his illness. Functional stability, they said, was likely conserved, though compositional stability was lost.

Smaller scale changes, Alm and his colleague added, could also affect microbiome composition, such as eating more fiber.

When Subject A ate more fiber one day, the researchers could, for the next day's sample, see an enrichment in fiber-sensitive species like those belonging to the Bifidobacteria, Roseburia, and Eubacterium genera.

Four Clostridiales OTUs, including Faecalibacterium prausnitzii, meanwhile were linked to eating citrus, and changes in Bifidobacteriales levels were associated with eating yogurt.

Interestingly, flossing was linked to a decrease of Streptococcus species, including the dental pathogen, S. mutans, in the saliva.

In their paper, the researchers noted that their study is limited by its small sample size and conservative analysis, but say that their work has opened up a number of questions. For instance, they wondered whether post-infection recovery is driven by ecological forces or by the host and whether the functional roles that taxa have affect their robustness, among others.

Going forward, Alm and his colleagues said they plan to investigate what keeps bacteria at their various average levels.

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